Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
1 non-index Markdown file with frontmatter.
target-specific fields are coherent.
Abstract oracle: fixture-independent property checks any run must satisfy.
eval.md declares properties and check type.
eval.md ↗Concrete cases: fixtures bound to expected values, run against the eval properties.
scenarios.md declares cases bound to fixtures.
scenarios.md ↗7 typed references; 0 resolver issues.
All on-demand references describe triggers.
Hypothesis references include verification.
Typed Mold references describe what casting consumes and when the generated skill should load each artifact.
Structured contract copied for validation or lookup.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Structured contract copied for validation or lookup.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Same draft with one additional step concretized (one loop iteration). Once every step is concrete, [[draft-next-step]] reports `draft: false` and the harness exits the loop.
Concrete gxformat2 workflow (`class: GalaxyWorkflow`) extracted from the fully-concretized draft at loop endstate via [[draft-extract]]: drafty steps dropped, `_plan_*` planning fields stripped, class promoted. The runnable, testable artifact that downstream Molds ([[implement-galaxy-workflow-test]], [[validate-galaxy-workflow]], [[run-workflow-test]]) consume.
Same ledger carried through the iteration: a blocking entry [[implement-galaxy-tool-step]] appended is routed to [[repair-galaxy-draft-topology]] and returns marked `resolved` or `surrendered`.
gxformat2 draft (see [[galaxy-workflow-draft-format]]) mutated in-place across iterations; topology is fully concrete, individual tool steps may still carry `TODO_*` sentinels and `_plan_*` planning fields.
Carried obligations ledger [[open-requirements-ledger]]: after implementing the chosen step, read it for a new `open` blocking entry [[implement-galaxy-tool-step]] appended (the step's declared output can't be computed from its wired inputs), and count open blocking entries for the escalation convergence gate.
Orchestrator Mold for the per-step Galaxy authoring loop. One invocation advances the gxformat2 draft by one step: pick → resolve a wrapper → summarize the wrapper → implement the step → validate. The harness loop reduces to while (gxwf draft-next-step <wf>).draft: invoke skill.
This Mold is single-entry, single-exit: it owns the loop oracle (draft-next-step) and the per-step validator (draft-validate --concrete). Iterations terminate when the draft has no remaining drafty steps; on that terminal call the Mold extracts the concrete galaxy-workflow.gxwf.yml (via draft-extract) — that promoted-class workflow, not the -draft file, is what downstream Molds test and run — and the harness then drops out of the loop and proceeds to terminal validation via validate-galaxy-workflow.
draft: false, the loop is done: run draft-extract to emit the concrete galaxy-workflow.gxwf.yml (drafty steps dropped, _plan_* stripped, class promoted to GalaxyWorkflow), then return. Otherwise carry the chosen step id forward.owner/repo path (Filter1, sort1, Cut1, Show beginning1, collection ops, __APPLY_RULES__):
Built-in / stock — the bare id is the wrapper identity; it does not route through discover-shed-tool (Tool Shed search) or author-galaxy-tool-wrapper. Only its concrete version needs resolving: the shed serves stock tools by bare id, but its TRS version-list endpoint can’t auto-resolve the version, so read it from a populated cache via galaxy-tool-cache list or take a known pin from the step plan — never hand-guess a stock version. summarize-galaxy-tool then performs the bare-id add/summarize with that explicit --tool-version.
Tool Shed wrapper — branch on whether the template already pinned wrapper identity (see the tiers in galaxy-workflow-draft-format):
tool_id is concrete and tool_version is TODO. Treat the pin as a strong seed: confirm it via discover-shed-tool and resolve the changeset, correcting the tool_id only if discovery contradicts the pin (a pinned id is high-confidence template evidence, not a guess to re-derive from scratch).tool_id is TODO. Search fresh: run discover-shed-tool against the step’s _plan_* context.Either way, if no acceptable shed candidate emerges, fall through to author-galaxy-tool-wrapper.
TODO_* / _plan_* slots into a concrete tool_id (confirming or correcting any pinned identity), tool_version, tool_state, and wrapper-determined port names.open blocking entry implement-galaxy-tool-step appended against this step — a declared output that can’t be computed from its wired inputs. draft-validate cannot catch this: the connection graph knows ports connect, not what they carry, so the draft validates green even though the step can’t run. If such an entry is present, escalate to repair-galaxy-draft-topology for a bounded repair (insert a producer/sub-path or honestly narrow the output); it marks the entry resolved, or surrendered when no producer is reachable. Each escalation must strictly reduce the open blocking-entry count, under a hard escalation cap; track both in the ledger’s topology_repair block (increment escalations, append the post-repair open count to open_history, surrender once escalations reaches cap). A surrendered entry stays open and is written into the final draft as a labelled gap rather than fabricated. Then return — the next iteration resumes the loop, realizing any draft-tier steps the repair inserted. With no new blocking entry, continue to validation.--concrete over the mutated draft. On green, return; the next iteration starts at step 1. On red, route per the failure-routing rules below.draft-validate --concrete failures fall into three buckets:
tool_state) — re-enter implement-galaxy-tool-step with the diagnostic._plan_* contract — wrong datatype, missing parameter, incompatible collection shape) — back out to step 2 and pick a different wrapper, either via discover-shed-tool with refined criteria or by escalating to author-galaxy-tool-wrapper.These are red-draft-validate buckets. The fourth escalation path — a step output uncomputable from its wired inputs — is not one of them: the draft validates green there, so it is detected from the ledger in step 5 above, not from a validation failure.
Consult galaxy-tool-job-failure-reference when the wrapper has explicit failure semantics that affect routing — strict-shell behavior, dynamic outputs, or non-default stdio rules can present as wrapper-choice mismatches even when the static shape validates.
Prior pipelines expressed the iteration as four entries: a discover-or-author branch plus summarize-galaxy-tool, implement-galaxy-tool-step, and validate-galaxy-step. Collapsing them into one orchestrator keeps the per-iteration narrative — including the discover-or-author branch and the failure-routing rules — in a single procedural surface that the cast skill can render coherently. Leaf Molds stay independently castable for ad-hoc invocation; only the pipeline shape changes.